MultiQC keeps failing on my Bacass. This is the

.command.sh

on my MULTIQC directory

#!/usr/bin/env bash
 
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
 
## Run MultiQC once to parse tool logs
multiqc -f -k yaml  .
 
## Collect additional files to be included in the report
if [ -d extra/ ]; then
    cp extra/* multiqc_data/
fi
 
## Create multiqc custom data
multiqc_to_custom_csv.py --assembly_type long
 
## Avoid the custom Multiqc table when the kmerfinder process is not invoked.
if grep ">skip_kmerfinder<" workflow_summary_mqc.yaml; then
    rm *_assembly_metrics_mqc.csv
fi
 
## Run multiqc a second time
multiqc -f -k yaml  .
 
cat <<-END_VERSIONS > versions.yml
"NFCORE_BACASS:BACASS:MULTIQC_CUSTOM":
    multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
END_VERSIONS

Here is my error

INFO:    Converting SIF file to temporary sandbox...

 

  /// MultiQC 🔍 | v1.19

 

|           multiqc | MultiQC Version v1.26 now available!

|           multiqc | Only using modules: custom_content, nanostat, porechop, pycoqc, kraken2, quast, prokka, bakta

|           multiqc | Excluding modules 'general_stats'

|           multiqc | Search path : /ibex/scratch/projects/c2303/work/4b/a367ac55713e66775958c6f86bbcb8

|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 152/152 

Matplotlib created a temporary cache directory at /tmp/matplotlib-b1k3xnnz because the default path (/home/pampum/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.

|    custom_content | nf-core-bacass-summary: Found 1 sample (html)

|          nanostat | Found 30 reports

|          porechop | Found 30 reports

|             quast | Found 2 reports

|            prokka | Found 1 logs

|           multiqc | Report      : multiqc_report.html

|           multiqc | Data        : multiqc_data

|           multiqc | Plots       : multiqc_plots

|           multiqc | MultiQC complete

cp: cannot create regular file 'multiqc_data/multiqc_kmerfinder.yaml': Disk quota exceeded

INFO:    Cleaning up image...

My Cluster’s IT team found that it was a permission’s issue with the multiqc folders, and suggested I run this

chmod g+s multiqc_data

but my question is, how do I get this to run before

cp extra/* multiqc_data/

is run from the

.command.sh

? Is there a way to modify

.nextflow.config

that would insert

chmod g+s multiqc_data

into this section of

.command.sh

?

## Collect additional files to be included in the report
if [ -d extra/ ]; then
    cp extra/* multiqc_data/
fi